Novel Antisense RNA and Epigenetic Regulation in Plant Abiotic Stress Responses

Plants respond and adapt to environmental stresses. Many stress-regulated genes have been identified and characterized. However, we think that novel RNA and epigenetic regulation mechanisms have additional functions in the regulation of plant stress responses.

We applied Arabidopsis tiling arrays to study the whole transcriptome under drought, cold, and high-salinity stress and identified about 7,000 stress-inducible, non-coding antisense RNAs. The majority of these antisense RNAs showed co-expression with their counterpart  sense mRNAs in response to stress. Accumulation of antisense RNA of a  drought-inducible  gene, RD29A, decreased in triple mutants of RDR1/2/6. RNA-seq revealed  that RDR-mediated antisense RNA synthesis occurs in genome-wide in response to drought stress. Most of the antisense RNA loci were not linked to smRNA generation. Accumulation of RDR-generated antisense RNAs increased in a 5’-3’ exoribonuclease mutant, xrn4, and decreased in a decapping enzyme mutant, dcp5, suggesting that the antisense RNAs are generated from degraded sense mRNAs. RNA decay rate analysis using RD29A sense mRNA showed that RDR1/2/6 functions in the degradation of the sense mRNAs. We propose a novel RNA regulation mechanism where RDR-mediated synthesis of antisense RNAs functions in the turnover of sense mRNAs under the stress.